Sirius is a

molecular modelling Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials scien ...

and analysis system developed at

San Diego Supercomputer Center The San Diego Supercomputer Center (SDSC) is an organized research unit of the University of California, San Diego. Founded in 1985, it was one of the five original NSF supercomputing centers. Its research pursuits are high performance comput ...

. Sirius is designed to support advanced user requirements that go beyond simple display of small

molecule A molecule is a group of two or more atoms that are held together by Force, attractive forces known as chemical bonds; depending on context, the term may or may not include ions that satisfy this criterion. In quantum physics, organic chemi ...

s and

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

s. Sirius supports high quality interactive

3D graphics 3D computer graphics, sometimes called CGI, 3D-CGI or three-dimensional computer graphics, are graphics that use a three-dimensional representation of geometric data (often Cartesian) that is stored in the computer for the purposes of perfor ...

, structure building, displaying

DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...

primary sequence Biomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function. The structure of these molecules may be considered at any of several length sca ...

s, access to remote data sources, and visualizing

molecular dynamics Molecular dynamics (MD) is a computer simulation method for analyzing the Motion (physics), physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamics ( ...

trajectories. It can be used for

scientific visualization Scientific visualization ( also spelled scientific visualisation) is an interdisciplinary branch of science concerned with the visualization of scientific phenomena. Michael Friendly (2008)"Milestones in the history of thematic cartography, st ...

and analysis, and

chemistry Chemistry is the scientific study of the properties and behavior of matter. It is a physical science within the natural sciences that studies the chemical elements that make up matter and chemical compound, compounds made of atoms, molecules a ...

and

biology Biology is the scientific study of life and living organisms. It is a broad natural science that encompasses a wide range of fields and unifying principles that explain the structure, function, growth, History of life, origin, evolution, and ...

instruction. This software is no longer supported as of 2011.

Key features

Sirius supports a variety of applications with a set of features, including: * Building and editing chemical structures using a library of fragments * Protein structure and

sequence alignment In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural biology, structural, or evolutionary relationships between ...

* Command line interpreter and scripting support fully compatible with extant

RasMol RasMol is a computer program written for molecular graphics visualization intended and used mainly to depict and explore biological macromolecule structures, such as those found in the Protein Data Bank (PDB). History It was originally develo ...

scripts * Full support for

trajectory visualizing * BLAST search directly in

Protein Data Bank The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which is overseen by the Worldwide Protein Data Bank (wwPDB). This structural data is obtained a ...

and

Uniprot UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived fro ...

databases * Ability to move parts of the loaded data while freezing the rest * Interactive calculation of

hydrogen bond In chemistry, a hydrogen bond (H-bond) is a specific type of molecular interaction that exhibits partial covalent character and cannot be described as a purely electrostatic force. It occurs when a hydrogen (H) atom, Covalent bond, covalently b ...

ing, steric clashes,

Ramachandran plot In biochemistry, a Ramachandran plot (also known as a Rama plot, a Ramachandran diagram or a �,ψplot), originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, is a way to visualize energetically allowed regio ...

s * Support for all major structure and sequence formats * Bundled

POV-Ray The Persistence of Vision Ray Tracer, most commonly acronymed as POV-Ray, is a cross-platform ray-tracing program that generates images from a text-based scene description. It was originally based on DKBTrace, written by David Kirk Buck and Aaro ...

for creating photorealistic images * Integrated selection and coloring across individual visualizing components Sirius is based on molecular graphics code and data structures developed as a part of the Molecular Biology Toolkit.

RasMol-compatible scripting

Sirius features a command line interpreter that can be used to quickly manipulate structure appearance and orientation. The set of commands has been patterned after

, so it's fully compatible with extant scripts. Added commands introduced in Sirius provide support for manipulating multiple structures loaded at the same time, and enable more flexible selection. Extant RasMol scripts can be imported and run within Sirius to produce high quality representations of encoded molecular scenes. Since RasMol uses a coordinate system that differs from that Sirius, internal conversion is performed when RasMol scripts are imported, so that any orientation changes are shown correctly. Any manually entered commands, however, are executed according to the Sirius coordinate system. Sirius supports several predefined atom-residue sets and color schemes, allows editing of scripts using the Command Panel interface, and logical operators and parentheses can be used to create complex selection commands.

Visualizing molecular dynamics trajectories

Sirius contains a full-featured molecular dynamics visualizing component. It can read output files from

AMBER Amber is fossilized tree resin. Examples of it have been appreciated for its color and natural beauty since the Neolithic times, and worked as a gemstone since antiquity."Amber" (2004). In Maxine N. Lurie and Marc Mappen (eds.) ''Encyclopedia ...

and

CHARMM Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them. The CH ...

simulations, including compressed and AMBER out files.

RMSD The root mean square deviation (RMSD) or root mean square error (RMSE) is either one of two closely related and frequently used measures of the differences between true or predicted values on the one hand and observed values or an estimator on th ...

changes along the trajectory can be calculated using user-defined atom subsets and displayed in an interactively updated graph. In order to reduce memory requirements, large multifile simulations may be loaded in a buffered mode. If a simulation involves changes in

fold, Sirius can be set to track and recompute displayed

secondary structure Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...

features in real time, which provides a convenient way to observe transformations of the structure. The full trajectory or selected frames can be exported as

QuickTime QuickTime (or QuickTime Player) is an extensible multimedia architecture created by Apple, which supports playing, streaming, encoding, and transcoding a variety of digital media formats. The term ''QuickTime'' also refers to the QuickTime Pla ...

video or a set of

scene snapshots that can later be converted to a high quality movie.

Access and download

Sirius is distributed freely from the project website to individuals affiliated with academic and non-profit organizations.Sirius downloads
/ref> Native desktop application installers are available for

Windows Windows is a Product lining, product line of Proprietary software, proprietary graphical user interface, graphical operating systems developed and marketed by Microsoft. It is grouped into families and subfamilies that cater to particular sec ...

Linux Linux ( ) is a family of open source Unix-like operating systems based on the Linux kernel, an kernel (operating system), operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically package manager, pac ...

, and

macOS macOS, previously OS X and originally Mac OS X, is a Unix, Unix-based operating system developed and marketed by Apple Inc., Apple since 2001. It is the current operating system for Apple's Mac (computer), Mac computers. With ...

References

{{Reflist

External links